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Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis

Overview of attention for article published in BMC Genomics, January 2016
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  • Above-average Attention Score compared to outputs of the same age (56th percentile)
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5 tweeters


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82 Mendeley
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Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis
Published in
BMC Genomics, January 2016
DOI 10.1186/s12864-015-2234-5
Pubmed ID

Josephine M. Bryant, Virginie C. Thibault, David G. E. Smith, Joyce McLuckie, Ian Heron, Iker A. Sevilla, Franck Biet, Simon R. Harris, Duncan J. Maskell, Stephen D. Bentley, Julian Parkhill, Karen Stevenson


Mycobacterium avium subspecies paratuberculosis (Map) is an infectious enteric pathogen that causes Johne's disease in livestock. Determining genetic diversity is prerequisite to understanding the epidemiology and biology of Map. We performed the first whole genome sequencing (WGS) of 141 global Map isolates that encompass the main molecular strain types currently reported. We investigated the phylogeny of the Map strains, the diversity of the genome and the limitations of commonly used genotyping methods. Single nucleotide polymorphism (SNP) and phylogenetic analyses confirmed two major lineages concordant with the former Type S and Type C designations. The Type I and Type III strain groups are subtypes of Type S, and Type B strains are a subtype of Type C and not restricted to Bison species. We found that the genome-wide SNPs detected provided greater resolution between isolates than currently employed genotyping methods. Furthermore, the SNP used for IS1311 typing is not informative, as it is likely to have occurred after Type S and C strains diverged and does not assign all strains to the correct lineage. Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) differentiates Type S from Type C but provides limited resolution between isolates within these lineages and the polymorphisms detected do not necessarily accurately reflect the phylogenetic relationships between strains. WGS of passaged strains and coalescent analysis of the collection revealed a very high level of genetic stability, with the substitution rate estimated to be less than 0.5 SNPs per genome per year. This study clarifies the phylogenetic relationships between the previously described Map strain groups, and highlights the limitations of current genotyping techniques. Map isolates exhibit restricted genetic diversity and a substitution rate consistent with a monomorphic pathogen. WGS provides the ultimate level of resolution for differentiation between strains. However, WGS alone will not be sufficient for tracing and tracking Map infections, yet importantly it can provide a phylogenetic context for affirming epidemiological connections.

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Mendeley readers

The data shown below were compiled from readership statistics for 82 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 1%
France 1 1%
Argentina 1 1%
Unknown 79 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 15 18%
Researcher 13 16%
Student > Master 8 10%
Student > Bachelor 7 9%
Student > Postgraduate 7 9%
Other 15 18%
Unknown 17 21%
Readers by discipline Count As %
Agricultural and Biological Sciences 19 23%
Biochemistry, Genetics and Molecular Biology 14 17%
Veterinary Science and Veterinary Medicine 10 12%
Immunology and Microbiology 8 10%
Medicine and Dentistry 4 5%
Other 6 7%
Unknown 21 26%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 28 June 2017.
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Altmetric has tracked 12,437,358 research outputs across all sources so far. This one is in the 42nd percentile – i.e., 42% of other outputs scored the same or lower than it.
So far Altmetric has tracked 7,364 research outputs from this source. They receive a mean Attention Score of 4.2. This one is in the 47th percentile – i.e., 47% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 334,988 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 56% of its contemporaries.
We're also able to compare this research output to 10 others from the same source and published within six weeks on either side of this one. This one has scored higher than 4 of them.